Dynastes hercules
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA987010 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome analysis of fat bodies of Dynastes hercules larvae.
| PRJDB16153 | ENA
Project description:Amendment of a thermophile-fermented compost to humus improves the growth of female larvae of the Hercules beetle, Dynastes hercules (Coleoptera: Scarabaeidae).
| PRJDB11803 | ENA
Project description:Mitochondrial genomes of ten Dynastes beetle species
| PRJNA813339 | ENA
Project description:mtDNA of the Satanas beetle, Dynastes satanas
| PRJNA1133938 | ENA
Project description:Miscanthus sacchariflorus cultivar:Hercules EF03(01-03) Genome sequencing
| PRJNA337643 | ENA
Project description:The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.
| S-EPMC9576211 | biostudies-literature
Project description:Amendment of a thermophile-fermented compost to humus improves the growth of female larvae of the Hercules beetle, Dynastes hercules (Coleoptera: Scarabaeidae)
| PRJDB11856 | ENA
Project description:Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several types of studies require long and accurate reads. In such cases researchers often combine both technologies and the erroneous long reads are corrected using the short reads. Current approaches rely on various graph or alignment based techniques and do not take the error profile of the underlying technology into account. Efficient machine learning algorithms that address these shortcomings have the potential to achieve more accurate integration of these two technologies. We propose Hercules, the first machine learning-based long read error correction algorithm. Hercules models every long read as a profile Hidden Markov Model with respect to the underlying platform's error profile. The algorithm learns a posterior transition/emission probability distribution for each long read to correct errors in these reads. We show on two DNA-seq BAC clones (CH17-157L1 and CH17-227A2) that Hercules-corrected reads have the highest mapping rate among all competing algorithms and have the highest accuracy when the breadth of coverage is high. On a large human CHM1 cell line WGS data set, Hercules is one of the few scalable algorithms; and among those, it achieves the highest accuracy.
| S-EPMC6265270 | biostudies-literature